printf("%s\t%d\t", name, i+1);
if (c[1] == c[2]) { // hom
if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
printf("%s\t%d\t", name, i+1);
if (c[1] == c[2]) { // hom
if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
size[0] = size_l; size[1] = size_r;
tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
size[0] = size_l; size[1] = size_r;
tot_len = n_ref = 0;
while ((l = seq_read_fasta(fp_fa, &seq, name, 0)) >= 0) {
tot_len = n_ref = 0;
while ((l = seq_read_fasta(fp_fa, &seq, name, 0)) >= 0) {